This notebook performs outlier-based QC for the non-genotyped large base editor screen, removing low outliers for the total count, low outliers for the number of detected features and high outliers for the percentage of counts from mitochondrial genes.
knitr::opts_chunk$set(
echo = FALSE,
message = FALSE,
warning = FALSE,
message = FALSE,
dev = "pdf",
dpi=300
)
library(Matrix)
library(ggplot2)
library(AnnotationHub)
library(AnnotationDbi)
library(scran)
library(scater)
library(grateful)
library(gridExtra)
folders_cellranger <- c("../cellranger/cellranger700_count_46539_7105STDY13259924_GRCh38-2020-A","../cellranger/cellranger700_count_46539_7105STDY13259926_GRCh38-2020-A")
file_name_mRNA_matrices <- "mRNA_matrices.rds"
file_name_mRNA_matrices_QC <- "mRNA_matrices_QC.rds"
file_name_sces <- "sce_list.rds"
ids <- c("CBE","ABE")
source("../../core_functions.R")
Number of cells before QC: 58673 In the ABE data set: 30226 In the CBE data set: 28447
Number of cells after QC: 56220 In the ABE data set: 28718 In the CBE data set: 27502